Biochemistry Exam 2 Review

What structural feature differentiates aldoses from ketoses? - Aldoses have an aldehyde group (-CHO) at carbon 1, while ketoses have a ketone group (C=O) at carbon 2.

How does the branching pattern of glycogen contribute to its function in energy storage? - The branching pattern increases solubility and allows for rapid release of glucose during energy demand.

Compare and contrast saturated and unsaturated fatty acids in terms of structure and function. - Saturated fatty acids lack double bonds, making them solid at room temp, while unsaturated fatty acids have kinks that prevent tight packing, making them liquid.

Why are phospholipids amphipathic, and how does this property contribute to membrane formation? - Phospholipids have a hydrophilic head and hydrophobic tails, allowing bilayer formation in aqueous environments.

What are the main components of the fluid mosaic model? - The bilayer consists of phospholipids, proteins, and cholesterol; proteins move laterally.

How does cholesterol impact membrane fluidity at different temperatures? - Cholesterol increases fluidity at low temperatures and decreases it at high temperatures.

Differentiate between peripheral and integral membrane proteins. - Peripheral proteins associate with the membrane surface, while integral proteins span the membrane.

How do lipid-anchored proteins remain associated with the membrane? - Lipid-anchored proteins are covalently bonded to lipids in the membrane.

What allows the potassium channel to be selective for K+ ions over Na+ ions? - The potassium channel has a selectivity filter that stabilizes K+ but not Na+ due to ion size and hydration energy.

Describe the movement of ions through a potassium channel in terms of concentration gradients. - Ions move through the channel down their concentration gradient without energy input.

How many Na+ and K+ ions are moved by the Na+/K+ pump per ATP hydrolyzed? - Three Na+ ions move out, and two K+ ions move in per ATP hydrolyzed.

Why is active transport necessary for maintaining cellular homeostasis? - Active transport maintains gradients necessary for nerve signaling and osmoregulation.

What are the three main steps in a signal transduction pathway? - Reception, transduction, and response.

What is the role of second messengers in signal transduction? - Second messengers amplify and distribute the signal inside the cell.

How do ligand-gated ion channels function? - These receptors open an ion channel upon ligand binding.

Compare receptor tyrosine kinases with G protein-coupled receptors in terms of structure and signaling. - RTKs dimerize and autophosphorylate; GPCRs activate G proteins to trigger cascades.

What happens when a ligand binds to a GPCR? - The GPCR undergoes a conformational change and activates a G protein.

How does the G protein cycle between active and inactive states? - G proteins bind GTP to become active and hydrolyze it to GDP to deactivate.

What is autophosphorylation, and why is it important for receptor tyrosine kinases? - Autophosphorylation activates downstream signaling proteins.

How do kinase cascades amplify a signal? - Kinase cascades amplify the original signal by phosphorylating multiple targets.

What structural features of ATP contribute to its high energy potential? - ATP has three negatively charged phosphate groups in close proximity.

How do electrostatic repulsion and resonance stabilization make ATP hydrolysis favorable? - Hydrolysis releases energy by relieving electrostatic repulsion and increasing entropy.

What is reaction coupling, and how does it allow unfavorable reactions to proceed? - Reaction coupling links favorable and unfavorable reactions through ATP hydrolysis.

How does ATP hydrolysis drive mechanical work in muscle contraction? - ATP hydrolysis powers myosin head movement in muscle contraction.

Identify the vitamin precursor for NAD+ and describe its role in metabolism. - Niacin is the precursor for NAD+, which carries electrons in redox reactions.

What is the function of FAD in redox reactions? - FAD accepts electrons and participates in redox reactions in metabolism.

In which steps of glycolysis is ATP produced? - ATP is produced in steps 7 and 10 of glycolysis.

What is substrate-level phosphorylation, and how does it contribute to ATP generation in glycolysis? - ATP forms directly from high-energy intermediates in glycolysis.

Why is NAD+ necessary for glycolysis to continue? - NAD+ is required for glycolysis to accept electrons from glyceraldehyde-3-phosphate.

How does lactic acid fermentation regenerate NAD+? - In lactic acid fermentation, pyruvate is reduced to lactate, regenerating NAD+.

What are the initial and final products of glycolysis? - Glycolysis converts glucose to pyruvate, producing ATP and NADH.

How does phosphofructokinase regulate glycolysis? - Phosphofructokinase is inhibited by ATP and activated by AMP, controlling glycolysis rate.

"I am the first to act, I occasionally steal a phosphate from ATP, and give it to those in need." - Identify the starting molecule, enzyme, and product: Glucose, hexokinase, glucose-6-phosphate.

"I am the enzyme that likes to flip sugar rings around, 6-membered structures with a phosphate should never exist. Glycolysis cannot proceed without me. Who am I?" - Identify the starting molecule, enzyme, and product: Glucose-6-phosphate, phosphoglucose isomerase, fructose-6-phosphate.

Why is it necessary for this isomerization reaction to occur? Why can’t biochemistry just phosphorylate G6P to form G1,6BP and follow through the cleavage step?: The isomerization allows the formation of a symmetrical molecule, fructose-1,6-bisphosphate, which is necessary for efficient cleavage in glycolysis.

Phosphofructokinase-1 (PFK-1) is the “Gatekeeper” of glycolysis. Categorize the following molecules as allosteric activators or inhibitors of PFK-1: ATP, AMP, ADP, Fructose 2,6 BP, PEP: Activators - AMP, ADP, Fructose 2,6 BP; Inhibitors - ATP, PEP.

Identify the two 3-carbon products in glycolysis and the enzyme that converts one to the other: Glyceraldehyde-3-phosphate (G3P) and dihydroxyacetone phosphate (DHAP); enzyme: triose phosphate isomerase.

Write the balanced chemical equation for the G3P dehydrogenase reaction. What type of reaction occurs here? (Oxidation, Reduction, Hydrolysis, Condensation, or Phosphorylation): G3P + NAD+ + Pi → 1,3-BPG + NADH + H+; Oxidation and phosphorylation.

What coenzyme is used in the reaction? Which is the oxidizing agent and which is the reducing agent?: Coenzyme: NAD+; Oxidizing agent: NAD+; Reducing agent: G3P.

Fill in the missing reactants and products: 1,3-BPG + ADP → (3-PG) + (ATP). Identify the type of reaction and the enzyme responsible for catalyzing it: Substrate-level phosphorylation; Enzyme: Phosphoglycerate kinase.

Compare substrate-level phosphorylation and oxidative phosphorylation: Substrate-level phosphorylation occurs directly via enzyme-catalyzed reactions, whereas oxidative phosphorylation relies on the electron transport chain and ATP synthase.

"I am a master of subtle moves, I shift phosphate groups from the 3rd position to the 2nd position, but I never add. What am I?" - Identify the enzyme and its function: Phosphoglycerate mutase; Moves the phosphate group from C3 to C2 of 3-phosphoglycerate to form 2-phosphoglycerate.

"I like to generate water. I can accomplish this by removing H and OH groups from 3-carbon molecules. Who am I?" - Identify the enzyme and reaction type: Enolase; Dehydration reaction.

Why is PEP a higher energy molecule compared to 2PG?: PEP has a high-energy enol-phosphate bond that is more unstable than the phosphate bond in 2PG.

Complete the reaction: PEP + ADP → Pyruvate + ATP. Identify the type of reaction catalyzed by pyruvate kinase: Substrate-level phosphorylation.

How many molecules of pyruvate, NADH, and water are generated from one molecule of glucose? Write out the net reaction for glycolysis: 2 pyruvate, 2 NADH, 2 H2O; Net reaction: Glucose + 2 NAD+ + 2 ADP + 2 Pi → 2 Pyruvate + 2 NADH + 2 ATP + 2 H2O + 2 H+.

Calculate the free energy change required for Na+ and Mg2+ movement into a cell given intracellular and extracellular concentrations: Requires Nernst equation application.

The G-protein associated with the 7TM-epinephrine/norepinephrine receptor acts on which enzyme? (Tyrosine Kinase, Adenylyl Cyclase, Protein Kinase A, or Phospholipase C): Adenylyl Cyclase.

Identify the type of transport exhibited by the following transporters:

Which G-protein subunit binds GTP, activating the protein? (Gα, Gβ, Gγ, or Gδ): Gα.

Describe the activation-inactivation cycle of a heterotrimeric transmembrane G-protein: Ligand binding activates GPCR → GPCR activates Gα by exchanging GDP for GTP → Gα dissociates and activates downstream signaling → GTP is hydrolyzed back to GDP, inactivating Gα.

Name the three main classes of transmembrane receptors and provide an example of each: GPCRs (e.g., β-adrenergic receptor), Receptor tyrosine kinases (e.g., insulin receptor), Ligand-gated ion channels (e.g., acetylcholine receptor).

Compare how cholesterol supports membrane structure at high vs. low temperatures: High temp - stabilizes membrane; Low temp - prevents solidification by disrupting phospholipid packing.

How do potassium channels selectively filter K+ over Na+, despite their similar charges?: The selectivity filter stabilizes K+ but not Na+ due to its size and hydration shell differences.

Identify the glycosidic linkage in a given disaccharide and determine whether it is a reducing sugar: Requires structural analysis.

An N-linked glycan is attached to Asn while an O-linked glycan is attached to Ser or Thr.

Differentiate glycoproteins from proteoglycans in terms of structure and function: Glycoproteins have shorter carbohydrate chains and function in signaling; Proteoglycans have longer chains and provide structural support.

Draw and identify the structure of an omega fatty acid, and specify its classification (omega-3, omega-6, etc.): Requires structural representation.

Compare the function and structural differences between sphingolipids, glycolipids, and cholesterol in the cell membrane: Sphingolipids provide insulation, glycolipids aid in cell recognition, and cholesterol modulates fluidity.

Draw the arrow-pushing mechanism for the ring-closing formation of glucose and fructose. Identify which is which: Requires structural representation.

Define and differentiate between enantiomers, diastereomers, epimers, and anomers: Enantiomers are mirror images; Diastereomers differ at multiple chiral centers; Epimers differ at one center; Anomers differ at the anomeric carbon.

Why must phosphoglycerate be converted from 3PG to 2PG before forming PEP?: Enables proper dehydration for high-energy phosphate bond formation in PEP.